[gmx-users] Re: dG/dl

David Mobley dmobley at gmail.com
Sun Nov 6 01:25:09 CET 2005

We are currently having some success here at UCSF reprocessing
trajectories with mdrun -rerun in different potentials. This allows us
to evaluate the potential energies needed for BAR. So far we've only
done this for fairly small systems though, so I'm not sure how
time-effective this will be for larger systems. Obviously Michael's
solution is better in the long run.

David Mobley

On 11/3/05, Michael Shirts <mrshirts at gmail.com> wrote:
> Hi, all-
> > I have tried the Bennett acceptance ratio method and did not
> > find significant differences with plain integration of dG/dlambda.
> > Although my experience is that people often take far too little
> > lambda points (the new soft-core lambda power of 1 in 3.3 helps a bit
> > tough). Michael, what is your opinion on this?
> I did a comparison of the various methods (except for slow growth, and
> there are links there that talk about slow growth) that was published
> in JCP earlier this year.
> M. R. Shirts and V. S. Pande. Comparison of efficiency and bias of
> free energies computer by exponential averaging, the Bennett
> acceptance ratio, and thermodynamic integration. Journal of Chemical
> Physics 122, 144107 (2005), PDF at:
> http://www.columbia.edu/~mrs2144/JChemPhys_122_144107.pdf
> Basically, if you are making vdW sites appear and disappear, Bennett
> will pretty much always be better.  I've made some modifications in
> GROMACS to make Bennett very trivial to run, but alas, haven't merged
> them yet -- a common problem with me.  I hope to get them merged as
> soon as I get caught up here in my posdoc, but that might not happen
> until Dec/early Jan.
> Best,
> Michael
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